. 2017 Jul 26;102(10):3635–3646. doi: 10.1210/jc.2017-00513

Table 2.

Bioinformatics Tools for 16S rRNA Gene–Sequencing and Metagenomic Shotgun–Sequencing Studies

Tools	Main Function	Reference	Web Site/Note
DADA^a	Denoising	107	sites.google.com.site/dadadenoiser
Denoiser^a	Denoising	108	qimme.org
ChimeraSlayer^a	Chimera detection	109	microbiomeutil.sourceforge.net
DECIPHER^a	Chimera detection	110	decipher.cee.wisr.edu
UCLUST^a	OTU clustering	111	www.drive5.com/usearch
CD-HIT-OTU^a	OTU clustering	112	weizhing-laboratory.ucsd.edu/cd-hit/otu
Mothur^a	ALL three steps^c	113	Mothur.org
QIIME^a	ALL three steps^c	114	qimme.org
MetaIDBA^b	Assembly	115	For short reads (75–150 bp)
MEGAN^b	Binning	116	Compositional-based
PhyloPythiaS^b	Binning	117	Similarity-based
MetaCluster^b	Binning	118	Both compositional-based and similarity-based
MetaGeneAnnotator^b	Functional annotation	119	metagene.nig.ac.jp/
METAREP^b	Functional annotation	120	jcvi.org/metarep/

^{^a}

Bioinformatics tools for 16S rRNA gene–sequencing studies.

^{^b}

Bioinformatics tools for Metagenomic shotgun–sequencing studies.

^{^c}

All three steps included in the general workflow of analysis for 16S rRNA gene–sequencing data.